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New Matter, Incorporation By Reference, Restriction and Claim Language for Nucleic Acid Molecules

New Matter, Incorporation By Reference, Restriction and Claim Language for Nucleic Acid Molecules. Julie Burke TC1600 QAS/PM 571-272-0512 julie.burke@uspto.gov. Objectives Potential Problems With Sequence Information New matter objections and rejections

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New Matter, Incorporation By Reference, Restriction and Claim Language for Nucleic Acid Molecules

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  1. New Matter, Incorporation By Reference, Restriction and Claim Language forNucleic Acid Molecules Julie Burke TC1600 QAS/PM 571-272-0512 julie.burke@uspto.gov

  2. Objectives • Potential Problems With Sequence Information • New matter objections and rejections • Incorporation by Reference- 37 CFR 1.57 • Examples • Reference to Tables • Improper Dependent Claims • Overview of 27 March 2007 OG Notice • Nucleic Acid Restriction Examples • Nucleic Acid Sequence Open versus Closed Language • Examination Practice for Combination Claims • Linking Claims • Summary Biotech training for nucleic acid sequences

  3. Potential Problems with Sequence Information In patent specifications, every element or ingredient of the product should be set forth in positive, exact, intelligible language, so that there will be no uncertainty as to what is meant. The relationship between sequence information submitted to a public database and the amino acid or nucleic acid product it identifies is sometimes indefinite, uncertain, and arbitrary. Biotech training for nucleic acid sequences

  4. Potential Problems with Sequence Information • The formula or characteristics of the sequence information submitted to the public database may change from time to time. • The changes may be made by • the person who initially submitted the sequence, • applicants or • third parties. • This uncertainty raises questions about • new matter • adequate written description • enablement • determining effective priority date • which version of the sequence may be entered by amendment and • which version of the sequence may be searched by STIC. Biotech training for nucleic acid sequences

  5. Two Statutes Governing New Matter There are two statutory provisions that prohibit the introduction of new matter: 35 U.S.C. 132 - No amendment shall introduce new matter into the disclosure of the invention; … 35  U.S.C. 251 - No new matter shall be introduced into the application for reissue. Biotech training for nucleic acid sequences

  6. New Matter Objections and Rejections When new matter is introduced into the specification, the amendment should be objected to under 35 U.S.C. 132 (35 U.S.C. 251 if a reissue application) and a requirement made to cancel the new matter. The subject matter which is considered to be new matter must be clearly identified by the examiner. If the new matter has been entered into the claims or affects the scope of the claims, the claims affected should be rejected under 35 U.S.C. 112, first paragraph, because the new matter is not described in the application as originally filed. Biotech training for nucleic acid sequences

  7. New Matter Guidance In the examination of an application following amendment thereof, the examiner must be on the alert to detect new matter. 35 U.S.C. 132 (a) should be employed as a basis for objection to amendments to the abstract, specification, or drawings attempting to add new disclosure to that originally disclosed on filing. See MPEP 706.03(o). The proscription against the introduction of new matter in a patent application (35 U.S.C. 132 and 251) serves to prevent an applicant from adding information that goes beyond the subject matter originally filed. See In re Rasmussen, 650 F.2d 1212, 1214, 211 USPQ 323, 326 (CCPA 1981). See MPEP 2105. Biotech training for nucleic acid sequences

  8. New Matter Added by Amendment All amendments or claims must find descriptive basis in the original disclosure, or they involve new matter. Applicant may rely for disclosure upon the specification with original claims and drawings, as filed. See also 37 CFR 1.121(f) and MPEP §  608.04. 37 CFR 1.121. Manner of making amendments in applications. ***** (f) No new matter . No amendment may introduce new matter into the disclosure of an application. Biotech training for nucleic acid sequences

  9. Relationship of Written Description and New Matter “Lack of written description is an issue that generally arises with respect to the subject matter of a claim. If an applicant amends or attempts to amend the abstract, specification or drawings of an application, an issue of new matter will arise if the content of the amendment is not described in the application as filed. Stated another way, information contained in any one of the specification, claims or drawings of the application as filed may be added to any other part of the application without introducing new matter.” MPEP 2163.06 Biotech training for nucleic acid sequences

  10. Reminder What is conventional or well known to one skilled in the art need not be disclosed in detail Vas-Cath, Inc. v. Mahurkar, 935 F.2d 1555, 19 USPQ2d 1111 (Fed. Cir. 1991). Biotech training for nucleic acid sequences

  11. Objectives • Potential Problems With Sequence Information • New matter objections and rejections • Incorporation by Reference- 37 CFR 1.57 • Examples • Reference to Tables • Improper Dependent Claims • Overview of 27 March 2007 OG Notice • Nucleic Acid Restriction Examples • Nucleic Acid Sequence Language • Open versus Closed Language • Other Language • Summary Biotech training for nucleic acid sequences

  12. Incorporation by Reference • Rule 37 CFR 1.57 • 69 FR 56482 (Sept. 21, 2004); 1287 OG 67 (Oct. 12, 2004) • for questions, contact Office of Patent Legal Administration • at (571) 272-7701 • Sequence Disclosure and Examples • Slides for initial BCP talk available at http://www.cabic.com/bcp/031505/ Biotech training for nucleic acid sequences

  13. 37 CFR 1.57(b) ….an incorporation by reference must be set forth in the specification and must: (1) Express a clear intent to incorporate by reference by using the root words “incorporat(e)” and “reference” (e.g., “incorporate by reference”); and (2) Clearly identify the referenced patent, application, or publication. Biotech training for nucleic acid sequences

  14. What is Clear Intent? • The examiner has the task of determining whether applicants clearly intended to incorporate material by reference. This must be determined upon a case-by-case basis. • In making the determination of clear intent the examiner will consider • language used in referencing the sequence • the context in which it is disclosed • any additional arguments/evidence presented by applicants. Biotech training for nucleic acid sequences

  15. What is Clear Intent? • A claim that identifies a sequence by database accession number will usually be accepted as clear intent to incorporate the sequence by reference. This claim must be an original claim that is present as of the filing date. • Language identifying a source only in passing as other prior work of no identified relevance is unlikely to be incorporated by reference. Biotech training for nucleic acid sequences

  16. 37 CFR 1.57 (c) “Essential material” may be incorporated by reference, but only by way of an incorporation by reference to a U.S. patent or U.S. patent application publication, which patent or patent application publication does not itself incorporate such essential material by reference…. Biotech training for nucleic acid sequences

  17. What is “Essential Material” Material that is necessary to meet requirements of 35 USC 112, 1st paragraph 35 USC 112, 2nd paragraph and/or 35 USC 112, 6th paragraph Biotech training for nucleic acid sequences

  18. 37 CFR 1.57 (d) Other material (“Nonessential material”) may be incorporated by reference to U.S. patents, U.S. patent application publications, foreign patents, foreign published applications, prior and concurrently filed commonly owned U.S. applications, or nonpatent publications. An incorporation by reference by hyperlink or other form of browser executable code is not permitted. Biotech training for nucleic acid sequences

  19. 37 CFR 1.57 (e) The examiner may require the applicant to supply a copy of the material incorporated by reference. If the Office requires the applicant to supply a copy of material incorporated by reference, the material must be accompanied by a statement that the copy supplied consists of the same material incorporated by reference in the referencing application. Biotech training for nucleic acid sequences

  20. 37 CFR 1.57 (f) Any insertion of material incorporated by reference into the specification or drawings of an application must be by way of an amendment to the specification or drawings. Such an amendment must be accompanied by a statement that the material being inserted is the material previously incorporated by reference and that the amendment contains no new matter. Biotech training for nucleic acid sequences

  21. What statements are required under 1.57(f)? A statement that the material being inserted is the material previously incorporated by reference and that the amendment contains no new matter is also required. 37 CFR 1.57(f). See also In re Hawkins, 486 F.2d 569, 179 USPQ 157 (CCPA 1973); In re Hawkins, 486 F.2d 579, 179 USPQ 163 (CCPA 1973); In re Hawkins, 486 F.2d 577, 179 USPQ 167 (CCPA 1973). Biotech training for nucleic acid sequences

  22. 37 CFR 1.57 (g)(1) A correction … is permitted only if the application as filed clearly conveys an intent to incorporate the material by reference. A mere reference to material does not convey an intent to incorporate the material by reference. Biotech training for nucleic acid sequences

  23. No Clear Intent? • If the examiner determines there was no clear intent to incorporate the sequence, the examiner will make and maintain 35 USC 112 rejection(s). • Final Rule “Discussion”indicates that “[i]f a reference to a document does not clearly indicate an intended incorporation by reference, examination will proceed as if no incorporation by reference statement has been made and the Office will not expend resources trying to determine if an incorporation by reference was intended.” [69 FR at 56500; 1287 OG at 82] Biotech training for nucleic acid sequences

  24. 37 CFR 1.57 (g)(2) A correction … is only permitted for material that was sufficiently described to uniquely identify the document. Biotech training for nucleic acid sequences

  25. What is “Uniquely Identify” A sequence which has only one version submitted prior to the filing date may be considered uniquely identified. If multiple versions of the sequence were submitted to the database prior to the effective filing date, the sequence may not be considered as uniquely identified. Biotech training for nucleic acid sequences

  26. Objectives • Potential Problems With Sequence Information • New matter objections and rejections • Incorporation by Reference- 37 CFR 1.57 • Examples • Reference to Tables • Improper Dependent Claims • Overview of 27 March 2007 OG Notice • Nucleic Acid Restriction Examples • Nucleic Acid Sequence Open versus Closed Language • Examination Practice for a Combination Claim • Linking Claims • Summary Biotech training for nucleic acid sequences

  27. Example 1: Effective Incorporation of Essential Material • Claim 1. Isolated Protein ABC. • The amino acid sequence of Protein ABC is considered essential material because it is necessary to meet the requirements of 35 U.S.C. 112, 1st and 2nd paragraphs. 37 CFR 1.57(c). • Upon review, the examiner noticed that the specification did not include the amino acid sequence for Protein ABC. However, the specification included the following statement: • “The amino acid sequence of Protein ABC has been disclosed as SEQ ID No 1 in U.S. Patent 6,123,456 and is hereby incorporated by reference.” • U.S. Patent 6,123,456 contains SEQ ID No 1. The requirements of 37 CFR 1.57 are met. Biotech training for nucleic acid sequences

  28. Example 2: Ineffective Incorporation of Essential Material • Original Claim 1. Isolated Protein ABC. • Upon review, the examiner noticed that the specification did not include the amino acid sequence for Protein ABC. However, the specification included the following statement: • “The amino acid sequence of Protein ABC has been disclosed as SEQ ID No 1 in U.S. Patent 6,123,456.” • The statement does not use the root words “incorporat(e)” and “reference” • The examiner uses FP 6.19.01 to require applicants to comply with 1.57(b)(1) and makes any corresponding rejections under 112, 1st, paragraph. Biotech training for nucleic acid sequences

  29. Example 2: Ineffective Incorporation of Essential Material (cont) FP 6.19.01 Ineffective Incorporation by Reference, General The attempt to incorporate subject matter into this application by reference to [1 ] is ineffective because [ 2 ]. Examiner Note 1. In bracket 1, identify the document such as an application or patent number or other identification. 2. In bracket 2, give reason(s) why it is ineffective (e.g., the root words "incorporate and/or "reference have been omitted, see 37 CFR 1.57(b)(1); the reference document is not clearly identified as required by 37 CFR 1.57(b)(2)). 3. This form paragraph should be followed by form paragraph 6.19.03. Biotech training for nucleic acid sequences

  30. Example 2: Ineffective Incorporation of Essential Material (cont) • Because Protein ABC is recited in an original claim, applicant may comply with 1.57(b)(1) by amending the specification under 1.57(g) as follows: • “The amino acid sequence of Protein ABC has been disclosed as SEQ ID No 1 in U.S. Patent 6,123,456 and is hereby incorporated by reference.” • Applicant must also respond to any other rejections or objections. • Best Practice Tip for Applicants: Recommend amending the specification to include SEQ ID No 1 and complying with the sequence requirements to help examiners identify prior art. Biotech training for nucleic acid sequences

  31. Example 3: Incorporation of Essential Material Claim 1. An isolated nucleic acid molecule encoding Protein ABC. The amino acid sequence of Protein ABC is considered essential material because it is necessary to meet the requirements of 35 U.S.C. 112, 1st paragraph. 37 CFR 1.57(c). Upon review, the examiner noticed that the specification did not include sequence for Protein ABC or for nucleic acid molecule which encoded Protein ABC. However, the specification included an incorporation by reference statement incorporating essential material submitted at GenBank. “The Protein ABC is encoded by the sequence of Gene ABC, which has been submittedat GenBank under Accession Number X-12345 and is incorporated by reference.” Biotech training for nucleic acid sequences

  32. Example 3: Incorporation of Essential Material (cont.) • Only one version of the sequence has been submittedunder Accession Number X-12345 prior to the filing date. • In an Office action, the examiner used FP 6.19 to require applicants to comply with 1.57(c) by • providing a copy of the essential material, • amending the specification to include the essential material, • providing a statement under 1.57(e) and/or (f). • If applicant adds the sequence, Applicant should also comply with the sequence requirements 37 CFR 1.821-1.825. Applicant should respond to any corresponding rejections under 112, 1st. Biotech training for nucleic acid sequences

  33. Example 3: Incorporation of Essential Material (cont.) FP 6.19 Incorporation by Reference, Unpublished U.S. Application, Foreign Patent or Application, Publication The incorporation of essential material in the specification by reference to an unpublished U.S. application, foreign application or patent, or to a publication is improper. Applicant is required to amend the disclosure to include the material incorporated by reference, if the material is relied upon to overcome any objection, rejection, or other requirement imposed by the Office. The amendment must be accompanied by a statement executed by the applicant, or a practitioner representing the applicant, stating that the material being inserted is the material previously incorporated by reference and that the amendment contains no new matter. 37 CFR 1.57(f). Biotech training for nucleic acid sequences

  34. Example 4: Non-essential Material Upon review of the specification, the examiner determined that the subject matter incorporated by reference to a sequence submittedto GenBank was “non-essential material” and therefore, did not object to the incorporation by reference. In reply to a non-final Office action, applicant filed an amendment to the claims to add a new limitation that was supported only by the GenBank deposit. The amendment filed by the applicant caused the examiner to re-determine that the incorporated subject matter was “essential material” under 37 CFR 1.57(c). The examiner rejected the claims that include the new limitation under 35 U.S.C. 112, first paragraph, in a final Office action. FP 6.19 was also included in the Office action. Biotech training for nucleic acid sequences

  35. Example 4: Non-essential Material (cont.) Because the rejection under 35 U.S.C. 112, first paragraph was necessitated by the applicant’s amendment, the finality of the Office action is proper. If the applicant wishes to overcome the rejection under 35 U.S.C. 112, first paragraph by filing an amendment under 37 CFR 1.57(f) to add the subject material disclosed in the GenBank into the specification, applicant may file the amendment as an after final amendment in compliance with 37 CFR 1.116. Alternatively, applicant may file an RCE under 37 CFR 1.114 accompanied by the appropriate fee, and an amendment per 37 CFR 1.57(f) within the time period for reply set forth in the final Office action. Biotech training for nucleic acid sequences

  36. Ex 5: Claim Refers to Database Accession Number Original Claim 1. A nucleic acid molecule of Genbank Accession No X- 23456. An original claim that identifies a sequence by database accession number will usually be accepted as clear intent to incorporate the sequence by reference. A sequence which has only one version submitted tothe database prior to the filing date may be considered uniquely identified. If multiple versions of the sequence were submitted prior to the effective filing date, the sequence may not be considered as uniquely identified. Biotech training for nucleic acid sequences

  37. Ex 5: Claim Refers to Database Accession Number Final Rule “Discussion”indicates that “[i]f a reference to a document does not clearly indicate an intended incorporation by reference, examination will proceed as if no incorporation by reference statement has been made and the Office will not expend resources trying to determine if an incorporation by reference was intended.” [69 FR at 56500; 1287 OG at 82] Use FP 6.19.01 to require applicants to comply with 1.57(b)(1) by adding root words “incorporat(e) and “reference” to the specification and to address 1.57(b)(2) as to whether the sequence was uniquely identified (only one version present in GenBank prior to the filing date). The Examiner also made corresponding rejections under 112 1st paragraph. Biotech training for nucleic acid sequences

  38. Ex 5: Claim Refers to Database Accession Number • In an Office action, the examiner also used FP 6.19 to require applicants to comply with 1.57(c) by • providing a copy of the essential material, • amending the specification to include the essential material, • providing a statement under 1.57(e) and/or (f). • Applicant should also comply with the sequence requirements 37 CFR 1.821-1.825 and any other rejections/objections. Biotech training for nucleic acid sequences

  39. Example 6: Reference to a Hyperlink • Upon review of the specification, the examiner noticed that the specification included an incorporation by reference statement incorporating essential material available at a website. • “The sequence has been submitted towww.geneseq.com.” • Because the source material exists on a hyperlink or other form of browser executable code, incorporation by reference is not permitted. See 37 CFR 1.57(d). The examiner would reject the claims under 35 USC 112, first paragraph. Applicant may incorporate by reference the sequence submitted toa website by • providing a copy of the essential material, • amending the specification to include the essential material, • providing a statement under 1.57(e) and/or (f). Biotech training for nucleic acid sequences

  40. Objectives • Potential Problems With Sequence Information • New matter objections and rejections • Incorporation by Reference- 37 CFR 1.57 • Examples • Reference to Tables • Improper Dependent Claims • Overview of 27 March 2007 OG Notice • Nucleic Acid Restriction Examples • Nucleic Acid Sequence Open versus Closed Language • Examination Practice for a Combination Claim • Linking Claims • Summary Biotech training for nucleic acid sequences

  41. Reference to Tables Where possible, claims are to be complete in themselves. Incorporation by reference to a specific figure or table “is permitted only in exceptional circumstances where there is no practical way to define the invention in words and where it is more concise to incorporate by reference than duplicating a drawing or table into the claim. Incorporation by reference is a necessity doctrine, not for applicant’s convenience.” Ex parte Fressola, 27 USPQ2d 1608, 1609 (Bd. Pat. App. & Inter. 1993) Biotech training for nucleic acid sequences

  42. Problem raised by reference to Tables • Claim 1. A nucleic acid molecule of Table 1. • Table 1. • What is the scope of the first nucleic acid molecule? • A nucleic acid molecule having SEQ ID No 1? • A nucleic acid molecule encoding SEQ ID No 4? • A nucleic acid which is 87% identical to human CARP gene? Biotech training for nucleic acid sequences

  43. Objectives • Potential Problems With Sequence Information • New matter objections and rejections • Incorporation by Reference- 37 CFR 1.57 • Examples • Reference to Tables • Improper Dependent Claims • Overview of 27 March 2007 OG Notice • Nucleic Acid Restriction Examples • Nucleic Acid Sequence Open versus Closed Language • Examination Practice for Combination Claim • Linking Claims • Summary Biotech training for nucleic acid sequences

  44. “Dependent” Claims Claim 1. An isolated nucleic acid molecule comprising SEQ ID No 1. Claim 2. An isolated nucleic acid molecule fragment comprising residues 1-30 of the molecule of claim 1. Claim 3. An isolated nucleic acid molecule comprising at least 70% sequence identity to the molecule of claim 1. Claim 4. An isolated nucleic acid molecule that hybridizes under stringent conditions to the molecule of claim 1. Claim 5. A polypeptide encoded by the isolated nucleic acid molecule of claim 1. Claim 6. An antibody which binds to the polypeptide of claim 5. Biotech training for nucleic acid sequences

  45. Test for Improper Dependent Claims The test for a proper dependent claim is whether the dependent claim includes every limitation of the parent claim. The test is not whether the claims differ in scope. A proper dependent claim shall not conceivably be infringed by anything which would not also infringe the basic claim. MPEP 608.01(n) Biotech training for nucleic acid sequences

  46. Objection of Improper Dependent Claims 7.36 Objection, 37 CFR 1.75(c), Improper Dependent Claim Claim [ 1 ] objected to under 37 CFR 1.75(c), as being of improper dependent form for failing to further limit the subject matter of a previous claim. Applicant is required to cancel the claim(s), or amend the claim(s) to place the claim(s) in proper dependent form, or rewrite the claim(s) in independent form. [ 2 ]. Biotech training for nucleic acid sequences

  47. Objectives • Potential Problems With Sequence Information • New matter objections and rejections • Incorporation by Reference- 37 CFR 1.57 • Examples • Reference to Tables • Improper Dependent Claims • Overview of 27 March 2007 OG Notice • Nucleic Acid Restriction Examples • Nucleic Acid Sequence Open versus Closed Language • Examination Practice for Combination Claims • Linking Claims • Summary Biotech training for nucleic acid sequences

  48. Official Gazette Notice 27 March 2007 In 1996, polynucleotide molecules were often claimed by simple reference to a nucleotide sequence (SEQ ID No). The 1996 OG Notice permitted examination of up to ten molecules described by their nucleotide sequence. See Examination of Patent Applications Containing Nucleotide Sequences, 1192 OG 68 (19 November 1996). Biotech training for nucleic acid sequences

  49. Official Gazette Notice 27 March 2007 (cont.) • Since 1996, the types of nucleic acid sequence-based claims have become more diverse and complex. Polynucleotide molecules are now often described in terms of • homology • percent identity • hybridization • variable positions specified within the sequence listing • function of the nucleic acid • partial linear nucleotide sequence • single nucleotide polymorphisms (SNPs) • the amino acid sequence of the protein encoded Biotech training for nucleic acid sequences

  50. Official Gazette Notice 27 March 2007 • The Office has reconsidered the policy set forth in the 1996 Notice in view of changes in • the complexity of applications filed, • the types of inventions claimed and • the state of the prior art in this technology. Biotech training for nucleic acid sequences

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